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2023

Conev, Anja and Rigo, Mauricio Menegatti and Devaurs, Didier and Fonseca, André Faustino and Kalavadwala, Hussain and de Freitas, Martiela Vaz and Clementi, Cecilia and Zanatta, Geancarlo and Antunes, Dinler Amaral and Kavraki, Lydia E. (2023) EnGens : a computational framework for generation and analysis of representative protein conformational ensembles. Briefings in Bioinformatics, 24 (4). bbad242. ISSN 1467-5463

2022

Conev, Anja and Devaurs, Didier and Rigo, Mauricio Menegatti and Antunes, Dinler Amaral and Kavraki, Lydia E. (2022) 3pHLA-score improves structure-based peptide-HLA binding affinity prediction. Scientific Reports, 12 (1). 10749. ISSN 2045-2322

Devaurs, Didier and Antunes, Dinler A. and Borysik, Antoni J. (2022) Computational modeling of molecular structures guided by hydrogen-exchange data. Journal of the American Society for Mass Spectrometry, 33 (2). pp. 215-237. ISSN 1044-0305

2021

Hall-Swan, Sarah and Devaurs, Didier and Rigo, Mauricio M. and Antunes, Dinler A. and Kavraki, Lydia E. and Zanatta, Geancarlo (2021) DINC-COVID : a webserver for ensemble docking with flexible SARS-CoV-2 proteins. Computers in Biology and Medicine, 139. 104943. ISSN 1879-0534

2020

Antunes, Dinler A. and Abella, Jayvee R. and Hall-Swan, Sarah and Devaurs, Didier and Conev, Anja and Moll, Mark and Lizée, Gregory and Kavraki, Lydia E. (2020) HLA-Arena : a customizable environment for the structural modeling and analysis of peptide-HLA complexes for cancer immunotherapy. JCO Clinical Cancer Informatics, 4. pp. 623-636. ISSN 2473-4276

Kravchenko, Oleksandr and Varava, Anastasiia and Pokorny, Florian T. and Devaurs, Didier and Kavraki, Lydia E. and Kragic, Danica (2020) A robotics-inspired screening algorithm for molecular caging prediction. Journal of Chemical Information and Modeling, 60 (3). pp. 1302-1316. ISSN 1549-9596

2019

Devaurs, Didier and Antunes, Dinler A and Hall-Swan, Sarah and Mitchell, Nicole and Moll, Mark and Lizée, Gregory and Kavraki, Lydia E (2019) Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins. BMC Molecular and Cell Biology, 20 (1). 42. ISSN 2661-8850

2018

Devaurs, Didier and Antunes, Dinler A. and Kavraki, Lydia E. (2018) Revealing unknown protein structures using computational conformational sampling guided by experimental hydrogen-exchange data. International Journal of Molecular Sciences, 19 (11). 3406. ISSN 1661-6596

Antunes, Dinler A. and Devaurs, Didier and Moll, Mark and Lizée, Gregory and Kavraki, Lydia E. (2018) General prediction of peptide-MHC binding modes using incremental docking : a proof of concept. Scientific Reports, 8. 4327. ISSN 2045-2322

2017

Devaurs, Didier and Antunes, Dinler A. and Papanastasiou, Malvina and Moll, Mark and Ricklin, Daniel and Lambris, John D. and Kavraki, Lydia E. (2017) Coarse-grained conformational sampling of protein structure improves the fit to experimental hydrogen-exchange data. Frontiers in Molecular Biosciences, 4. 13. ISSN 2296-889X

2016

Devaurs, Didier and Siméon, Thierry and Cortés, Juan (2016) Optimal path planning in complex cost spaces with sampling-based algorithms. IEEE Transactions on Automation Science and Engineering, 13 (2). pp. 415-424. ISSN 1545-5955

2015

Devaurs, Didier and Molloy, Kevin and Vaisset, Marc and Shehu, Amarda and Siméon, Thierry and Cortés, Juan (2015) Characterizing energy landscapes of peptides using a combination of stochastic algorithms. IEEE Transactions on NanoBioscience, 14 (5). pp. 545-552. ISSN 1536-1241

Devaurs, Didier and Shehu, Amarda and Siméon, Thierry and Cortés, Juan; Zheng, Huiru and Dubitzky, Werner and Hu, Xiaohua and Hao, Jin-Kao and Berrar, Daniel and Cho, Kwang-Hyun and Wang, Yadong and Gilbert, David, eds. (2015) Sampling-based methods for a full characterization of energy landscapes of small peptides. In: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, GBR, pp. 37-44. ISBN 9781479956692

2013

Devaurs, Didier and Bouard, Léa and Vaisset, Marc and Zanon, Christophe and Al-Bluwi, Ibrahim and Iehl, Romain and Siméon, Thierry and Cortés, Juan (2013) MoMA-LigPath : a web server to simulate protein-ligand unbinding. Nucleic Acids Research, 41 (W1). W297-W302. ISSN 0305-1048

2009

Gras, Robin and Devaurs, Didier and Wozniak, Adrianna and Aspinall, Adam (2009) An individual-based evolving predator-prey ecosystem simulation using a fuzzy cognitive map as the behavior model. Artificial Life, 15 (4). pp. 423-463. ISSN 1530-9185